Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles

First evaluation of the microbiome of built cultural heritage by using the Ion Torrent next generation sequencing platform

(2018) Justyna Adamiak et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

Comparison of methods for identification of microbial communities in book collections: Culture-dependent (sequencing and MALDI-TOF MS) and culture-independent (Illumina MiSeq)

(2018) Lucia Kraková et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

TaqMan qPCR pushes boundaries for the analysis of millennial wood

(2017) Javier Gómez-Zeledón et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ritual complexity in a past community revealed by ancient DNA analysis of pre-colonial terracotta items from Northern Ghana

(2017) Heather A. Robinson et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Farmer fidelity in the Canary Islands revealed by ancient DNA from prehistoric seeds

(2017) Jenny Hagenblad et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Comparing ancient DNA survival and proteome content in 69 archaeological cattle tooth and bone samples from multiple European sites

(2017) Caroline Wadsworth et al.   Journal of Proteomics

Ancient DNA analysis identifies marine mollusc shells as new metagenomic archives of the past

(2017) Clio Der Sarkissian et al.   Molecular Ecology Resources

Phylogenomics using formalin-fixed and 100+ year-old intractable natural history specimens

(2017) Sara Ruane et al.   Molecular Ecology Resources

Eggshell palaeogenomics: Palaeognath evolutionary history revealed through ancient nuclear and mitochondrial DNA from Madagascan elephant bird ( Aepyornis sp.) eggshell

(2017) Alicia Grealy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus

(2017) Laura S. Weyrich et al.   NATURE

Single-stranded DNA library preparation from highly degraded DNA usingT4DNA ligase

(2017) Marie-Theres Gansauge et al.   NUCLEIC ACIDS RESEARCH

A new model for ancient DNA decay based on paleogenomic meta-analysis

(2017) Logan Kistler et al.   NUCLEIC ACIDS RESEARCH

Identification of HPV Types and Mycobacterium Tuberculosis Complex in Historical Long-Term Preserved Formalin Fixed Tissues in Different Human Organs

(2017) Maja Hühns et al.   PLoS One

A molecular portrait of maternal sepsis from Byzantine Troy

(2017) Alison M Devault et al.   eLife

Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum

(2017) Henrik B. Hansen et al.   PLoS One

Successful enrichment and recovery of whole mitochondrial genomes from ancient human dental calculus

(2016) Andrew T. Ozga et al.   AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY

Museomics resolve the systematics of an endangered grass lineage endemic to north-western Madagascar

(2016) Christian Silva et al.   ANNALS OF BOTANY

Genome Sequence of a 5,310-Year-Old Maize Cob Provides Insights into the Early Stages of Maize Domestication

(2016) Jazmín Ramos-Madrigal et al.   CURRENT BIOLOGY

Insights into human evolution from ancient and contemporary microbiome studies

(2016) Stephanie L Schnorr et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Ancient DNA in historical parchments - identifying a procedure for extraction and amplification of genetic material

(2016) T. Lech   GENETICS AND MOLECULAR RESEARCH

Finding Britain's last hunter-gatherers: A new biomolecular approach to ‘unidentifiable’ bone fragments utilising bone collagen

(2016) Sophy Charlton et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Reviving Galápagos snails: ancient DNA extraction and amplification from shells of probably extinct endemic land snails

(2016) Fernando A. Villanea et al.   JOURNAL OF MOLLUSCAN STUDIES

Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley

(2016) Martin Mascher et al.   NATURE GENETICS

A protocol for subsampling Late Quaternary coprolites for multi-proxy analysis

(2016) Jamie R. Wood et al.   QUATERNARY SCIENCE REVIEWS

Single-strand DNA library preparation improves sequencing of formalin-fixed and paraffin-embedded (FFPE) cancer DNA

(2016) Mathias Stiller et al.   Oncotarget

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Protein sequences bound to mineral surfaces persist into deep time

(2016) Beatrice Demarchi et al.   eLife

Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens

(2016) Clemens L. Weiß et al.   Royal Society Open Science

The efficacy of high-throughput sequencing and target enrichment on charred archaeobotanical remains

(2016) H. M. Nistelberger et al.   Scientific Reports

New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA

(2015) Nathan Wales et al.   BIOTECHNIQUES

Ancient DNA unravels the truth behind the controversial GUS Greenlandic Norse fur samples: the bison was a horse, and the muskox and bears were goats

(2015) Mikkel-Holger S. Sinding et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ancient DNA analysis of dental calculus

(2015) Laura S. Weyrich et al.   JOURNAL OF HUMAN EVOLUTION

Ancient human microbiomes

(2015) Christina Warinner et al.   JOURNAL OF HUMAN EVOLUTION

Natural history collections-based research: progress, promise, and best practices

(2015) Bryan S. McLean et al.   JOURNAL OF MAMMALOGY

Comparing the performance of three ancient DNA extraction methods for high-throughput sequencing

(2015) Cristina Gamba et al.   Molecular Ecology Resources

Museums: The endangered dead

(2015) Christopher Kemp   NATURE

Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting

(2015) Sarah Fiddyment et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification

(2015) Kirsten A. Ziesemer et al.   Scientific Reports

Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa

(2015) Lee R Berger et al.   eLife

Metabolomic and high-throughput sequencing analysis—modern approach for the assessment of biodeterioration of materials from historic buildings

(2015) Beata Gutarowska et al.   Frontiers in Microbiology

Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone

(2015) Ron Pinhasi et al.   PLoS One

Detection of Cytosine Methylation in Ancient DNA from Five Native American Populations Using Bisulfite Sequencing

(2015) Rick W. A. Smith et al.   PLoS One

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

(2015) Sarah M. Hykin et al.   PLoS One

Retroviral DNA Sequences as a Means for Determining Ancient Diets

(2015) Jessica I. Rivera-Perez et al.   PLoS One

Viruses in a 14th-Century Coprolite

(2014) S. Appelt et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)

(2014) Anna-Sapfo Malaspinas et al.   BIOINFORMATICS

Rodents of the Caribbean: origin and diversification of hutias unravelled by next-generation museomics

(2014) P.-H. Fabre et al.   Biology Letters

Ancient DNA reveals prehistoric habitat fragmentation and recent domestic introgression into native wild reindeer

(2014) Knut H. Røed et al.   CONSERVATION GENETICS

Unmasking the measles-like parchment discoloration: molecular and microanalytical approach

(2014) Guadalupe Piñar et al.   ENVIRONMENTAL MICROBIOLOGY

Ancient DNA sheds new light on the Svalbard foraminiferal fossil record of the last millennium

(2014) J. Pawłowska et al.   Geobiology

Proteomics evidence for kefir dairy in Early Bronze Age China

(2014) Yimin Yang et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Herbarium specimens reveal a historical shift in phylogeographic structure of common ragweed during native range disturbance

(2014) Michael D. Martin et al.   MOLECULAR ECOLOGY

Pathogens and host immunity in the ancient human oral cavity

(2014) Christina Warinner et al.   NATURE GENETICS

Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing

(2014) M. D. Teasdale et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

(2014) C. Warinner et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Using archaeogenomic and computational approaches to unravel the history of local adaptation in crops

(2014) R. G. Allaby et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

An Integrated Approach to the Taxonomic Identification of Prehistoric Shell Ornaments

(2014) Beatrice Demarchi et al.   PLoS One

Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes

(2014) Martin Laurence et al.   PLoS One

Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

(2014) Raul J. Cano et al.   PLoS One

A Biological Stone from a Medieval Cemetery in Poland

(2014) Judyta J. Gładykowska-Rzeczycka et al.   PLoS One

An epigenetic window into the past?

(2014) L. Orlando et al.   SCIENCE

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

(2014) D. Gokhman et al.   SCIENCE

Ancient DNA reveals elephant birds and kiwi are sister taxa and clarifies ratite bird evolution

(2014) K. J. Mitchell et al.   SCIENCE

Unlocking Ancient Protein Palimpsests

(2014) E. Cappellini et al.   SCIENCE

Recovery of a Medieval Brucella melitensis Genome Using Shotgun Metagenomics

(2014) G. L. Kay et al.   mBio

Genome flux and stasis in a five millennium transect of European prehistory

(2014) Cristina Gamba et al.   Nature Communications

Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process

(2014) Oliver Smith et al.   Scientific Reports

Direct evidence of milk consumption from ancient human dental calculus

(2014) C. Warinner et al.   Scientific Reports

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

Pulling out the 1%: Whole-Genome Capture for the Targeted Enrichment of Ancient DNA Sequencing Libraries

(2013) Meredith L. Carpenter et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Comparison of protocols for DNA extraction from long-term preserved formalin fixed tissues

(2013) Stefan Paireder et al.   ANALYTICAL BIOCHEMISTRY

Phenotypes from ancient DNA: Approaches, insights and prospects

(2013) Gloria G. Fortes et al.   BIOESSAYS

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters

(2013) Hákon Jónsson et al.   BIOINFORMATICS

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

(2013) J. S. Pedersen et al.   GENOME RESEARCH

Searching for Scandinavians in pre-Viking Scotland: molecular fingerprinting of Early Medieval combs

(2013) Isabella C.C. von Holstein et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Unlocking the vault: next-generation museum population genomics

(2013) Ke Bi et al.   MOLECULAR ECOLOGY

A mitochondrial genome sequence of a hominin from Sima de los Huesos

(2013) Matthias Meyer et al.   NATURE

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

(2013) Christina J Adler et al.   NATURE GENETICS

Resolving lost herbivore community structure using coprolites of four sympatric moa species (Aves: Dinornithiformes)

(2013) J. R. Wood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments

(2013) J. Dabney et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-Generation Museomics Disentangles One of the Largest Primate Radiations

(2013) Katerina Guschanski et al.   SYSTEMATIC BIOLOGY

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol

(2013) Jeremy Miller et al.   ZooKeys

A Lost Link between a Flightless Parrot and a Parasitic Plant and the Potential Role of Coprolites in Conservation Paleobiology

(2012) Jamie R. Wood et al.   CONSERVATION BIOLOGY

Minimally destructive DNA extraction from archaeological artefacts made from whale baleen

(2012) Mikkel-Holger S. Sinding et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Next generation sequencing of DNA in 3300-year-old charred cereal grains

(2012) Sandra L. Bunning et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

High-Resolution Analysis of Cytosine Methylation in Ancient DNA

(2012) Bastien Llamas et al.   PLoS One

High-Resolution Coproecology: Using Coprolites to Reconstruct the Habits and Habitats of New Zealand’s Extinct Upland Moa (Megalapteryx didinus)

(2012) Jamie R. Wood et al.   PLoS One

DNA Extraction from Museum Specimens of Parasitic Hymenoptera

(2012) Jeremy C. Andersen et al.   PLoS One

Insights from Characterizing Extinct Human Gut Microbiomes

(2012) Raul Y. Tito et al.   PLoS One

The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils

(2012) M. E. Allentoft et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Clovis Age Western Stemmed Projectile Points and Human Coprolites at the Paisley Caves

(2012) D. L. Jenkins et al.   SCIENCE

DNA Extraction From Orthoptera Museum Specimens

(2011) Marcello Tagliavia et al.   ANALYTICAL LETTERS

The blossoming of plant archaeogenetics

(2011) Sarah A. Palmer et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

DNA in ancient bone – Where is it located and how should we extract it?

(2011) Paula F. Campos et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

mapDamage: testing for damage patterns in ancient DNA sequences

(2011) Aurelien Ginolhac et al.   BIOINFORMATICS

Ancient DNA confirms a local origin of domesticated chenopod in eastern North America

(2011) Logan Kistler et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ancient bacterial DNA (aDNA) in dental calculus from archaeological human remains

(2011) Hans R. Preus et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Aspects of ancient Greek trade re-evaluated with amphora DNA evidence

(2011) Brendan P. Foley et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ancient DNA Recovers the Origins of Māori Feather Cloaks

(2011) K. Hartnup et al.   MOLECULAR BIOLOGY AND EVOLUTION

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

DNA Damage in Plant Herbarium Tissue

(2011) Martijn Staats et al.   PLoS One

A novel and non-destructive approach for ZooMS analysis: ammonium bicarbonate buffer extraction

(2011) Nienke Laura van Doorn et al.   Archaeological and Anthropological Sciences

Characterising the potential of sheep wool for ancient DNA analyses

(2011) Luise Ørsted Brandt et al.   Archaeological and Anthropological Sciences

Analysis of ancient human genomes

(2010) Beth Shapiro et al.   BIOESSAYS

Direct PCR amplification and sequencing of specimens' DNA from preservative ethanol

(2010) Shadi Shokralla et al.   BIOTECHNIQUES

A flock of sheep, goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture

(2010) Michael G. Campana et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Ancient DNA, a Neolithic legging from the Swiss Alps and the early history of goat

(2010) Angela Schlumbaum et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Survival and recovery of DNA from ancient teeth and bones

(2010) C.J. Adler et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate

(2010) J. H. SØNSTEBØ et al.   Molecular Ecology Resources

Ancient human genome sequence of an extinct Palaeo-Eskimo

(2010) Morten Rasmussen et al.   NATURE

Ancient mitochondrial DNA analysis reveals complexity of indigenous North American turkey domestication

(2010) C. F. Speller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fossil avian eggshell preserves ancient DNA

(2010) C. L. Oskam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Amino acid racemization dating of marine shells: A mound of possibilities

(2010) Beatrice Demarchi et al.   QUATERNARY INTERNATIONAL

Targeted Investigation of the Neandertal Genome by Array-Based Sequence Capture

(2010) H. A. Burbano et al.   SCIENCE

High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil

(2009) Jianghai Lin et al.   ANALYTICAL BIOCHEMISTRY

Analysis of complete mitochondrial genomes from extinct and extant rhinoceroses reveals lack of phylogenetic resolution

(2009) Eske Willerslev et al.   BMC EVOLUTIONARY BIOLOGY

A nondestructive method for obtaining maternal DNA from avian eggshells and its application to embryonic viability determination in herring gulls (Larus argentatus)

(2009) C. EGLOFF et al.   Molecular Ecology Resources

A rapid column-based ancient DNA extraction method for increased sample throughput

(2009) NADIN ROHLAND et al.   Molecular Ecology Resources

Searching for DNA in museum specimens: a comparison of sources in a mammal species

(2009) M. CASAS-MARCE et al.   Molecular Ecology Resources

Non-Destructive Sampling of Ancient Insect DNA

(2009) Philip Francis Thomsen et al.   PLoS One

Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation

(2009) Sarah A. Palmer et al.   PLoS One

Is amino acid racemization a useful tool for screening for ancient DNA in bone?

(2009) M. J. Collins et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Degradation of biomolecules in artificially and naturally aged teeth: Implications for age estimation based on aspartic acid racemization and DNA analysis

(2008) Reimer C. Dobberstein et al.   FORENSIC SCIENCE INTERNATIONAL

DNA damage in preserved specimens and tissue samples: a molecular assessment

(2008) Juergen Zimmermann et al.   Frontiers in Zoology

Improved methodology for extraction and amplification of DNA from single grains of charred wheat

(2008) Rachel J. Giles et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Molecular paleoparasitological diagnosis of Ascaris sp. from coprolites: new scenery of ascariasis in pre-Colombian South America times

(2008) Daniela Leles et al.   MEMORIAS DO INSTITUTO OSWALDO CRUZ

Preservation of ancient DNA in thermally damaged archaeological bone

(2008) Claudio Ottoni et al.   NATURWISSENSCHAFTEN

Amplification of cox2 (~620 bp) from 2 mg of Up to 129 Years Old Herbarium Specimens, Comparing 19 Extraction Methods and 15 Polymerases

(2008) Sabine Telle et al.   PLoS One

Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

(2008) Raúl Y. Tito et al.   PLoS One

Coprolite deposits reveal the diet and ecology of the extinct New Zealand megaherbivore moa (Aves, Dinornithiformes)

(2008) J WOOD et al.   QUATERNARY SCIENCE REVIEWS

DNA from Pre-Clovis Human Coprolites in Oregon, North America

(2008) M. T. P. Gilbert et al.   SCIENCE

Ancient DNA fragments inside Classical Greek amphoras reveal cargo of 2400-year-old shipwreck

(2007) Maria C. Hansson et al.   JOURNAL OF ARCHAEOLOGICAL SCIENCE

Extracting DNA from museum bird eggs, and whole genome amplification of archive DNA

(2007) PATRICIA L. M. LEE et al.   Molecular Ecology Resources